I bought a 3DP-12 last year. Assembled it and had a great time running lots of prints and doing some minor upgrades,hot end replacement, etc. All was going very well until I decided to take it apart for routine cleaning and maintenance lubing the rods, screws, and cable management. When I reassembled the printer and I went to auto home and both the x and y axis where running in reverse. Strange thing is that I didn’t ever unplug the stepper connections on the board. I only unplugged the motor connections, which are keyed to prevent reversal. Has anyone ever seen this type of behavior?

I had previously flashed an upgrade to 1.1.0 RC8 with good results. During the my most recent re-build I did take the opportunity to upgrade to a sub-version of RC8 created by Dark Dragon Wing (https://www.thingiverse.com/thing:2116377/#files). This is when the problem first appeared. After some initial troubleshooting I decided to revert to my original version of RC8. However, the problem persisted. I am really stumped, I am back to a proven firmware version and I really don't think there is a problem with the wiring. Could there be some glitch in the way I am flashing the firmware with Arduino? Missing reference files or what-not? I really don't know anything about Arduino.

I know that on occasion when re-flashing sometimes the EEProm are not cleared of data that can cause the new firmware to act strangely.

If you have enabled EEPROM in configuration.h
I clear errors by sending M502 (Factory Reset) and a M500 (Store Settings) or more simply stated a factory reset and the problem went away.

Once I flashed the new Firmware and would not work correctly until I had factory reset the 3D Printer using the above technique multiple times, Between flashes. However after that the Controller kicked the can. ( Would reboot during every print ) hardware thermal issue, not firmware.

Just to report back as promised - I did clear/reset as instructed but with no joy. Some additional troubleshooting helped me determine that the Y-axis is ok. Direction of travel and limit switch trigger is correct. Z-axis is running in the normal direction, but the board is not recognizing my new inductive proximity switch. It triggers, as indicated by led, but the signal is not picked up by the board and travel continues/crashes. Finally, I have my crazy X-axis which is clearly running in reverse with similar limit switch behavior. I am starting to wonder if this is somehow linked to my new Z-axis proximity switch. Its really the only new element in the setup. I am going to try it without the new inductive probe and see what happens!

Looking at you configuration file custom name is limited to 13 characters for MLCD2004 Displays or they will cause the top line to display incorrectly.

#define CUSTOM_MACHINE_NAME "DKDGWi HICTOP 3DPDK" // DKDGWi

As you have not provided us with your Proximity sensor make or model, will explain using my proximity sensor.
The Z-Axis is proximity sensor is controlled by the following lines shown are my settings used with a Normally Closed "TL-W3MC2 " Proximity Sensor
// Mechanical endstop with COM to ground and NC to Signal uses "false" here (most common setup).
#define Z_MIN_ENDSTOP_INVERTING false // set to true to invert the logic of the endstop.
#define Z_MIN_PROBE_ENDSTOP_INVERTING false // set to same logic as "Z_MIN_ENDSTOP_INVERTING".